Thank you for the additional information.
I am getting confused on what you are telling me, so allow me to explain what I need you to check for me and report that so I can help you.
We need to set the mark on the flywheel so it appears in the window. Turn the crank to get that to happen. For this entire operation, any time we need to turn the crankshaft, make sure both spark plugs are removed and stay removed. Since we are not sure if the cam(s) are in time, we want to minimize as much resistance to turning as possible. That was it is easy to tell if something is wrong.
While we are turning the crankshaft, we need to watch the Intake valve on the rear cylinder open (go down) then close (come back up). Once you see the intake valve close (stop moving up) now look for the TDC mark on the flywheel in the window. This is all we are focusing on at this time. Once you have that mark visible in the window, look for the mark on the cam gear and see if it lines up with the reference mark on the cylinder head. If the TDC mark on the flywheel is visible in the window and the reference mark on the cam and head line up, the cylinder is in time.
Yamaha makes a big deal about making sure the intermediate gear is timed, but the truth of the matter is it does not matter. In timing cams, the only critical factor is when the valve is being opened relative to where the piston is in its travel. I mention this because you said something about marking the cam chain and trying to get it back where it was. Although a noble intent, if I understand what you did, it may not have been necessary.
Since you had the flywheel off, I am guessing you did not alter the cam timing for the front cylinder, so it should be ok.
Check that out and let me know if you need more help.
PS, under no circumstances should you ever force the crank to turn. IF it offers unexpected resistance, stop and look things over. If you force it you could bend a valve creating an even bigger problem. If you feel the rotation get hard or stop, turn the crank backwards a little bit and see if you see a valve trying to open, and look down the cylinder and see if the piston is trying to come up. If it is, back it off and take the gear of the cam and start from there setting the cam timing from scratch.
it appears in the win